3E5P

Crystal structure of alanine racemase from E.faecalis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.232 

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Literature

Structural insights into the alanine racemase from Enterococcus faecalis.

Priyadarshi, A., Lee, E.H., Sung, M.W., Nam, K.H., Lee, W.H., Kim, E.E., Hwang, K.Y.

(2009) Biochim Biophys Acta 1794: 1030-1040

  • DOI: 10.1016/j.bbapap.2009.03.006
  • Primary Citation of Related Structures:  
    3E5P, 3E6E

  • PubMed Abstract: 

    • Alanine racemase (AlaR) is a bacterial enzyme that belongs to the fold-type III group of pyridoxal 5'-phosphate (PLP)-dependent enzymes. AlaR catalyzes the interconversion between L- and D-alanine, which is important for peptidoglycan biosynthesis. This enzyme is common in prokaryotes, but absent in eukaryotes, which makes it an attractive target for the design of new antibacterial drugs ...

    Alanine racemase (AlaR) is a bacterial enzyme that belongs to the fold-type III group of pyridoxal 5'-phosphate (PLP)-dependent enzymes. AlaR catalyzes the interconversion between L- and D-alanine, which is important for peptidoglycan biosynthesis. This enzyme is common in prokaryotes, but absent in eukaryotes, which makes it an attractive target for the design of new antibacterial drugs. Here, we report the crystal structures of both the apoenzyme and the d-cycloserine (DCS) complex of AlaR from the pathogenic bacterium Enterococcus faecalis v583, at a resolution of 2.5 A. DCS is a suicide inhibitor of AlaR and, as such, serves as an antimicrobial agent and has been used to treat tuberculosis and urinary tract infection-related diseases, and makes several hydrogen bonds with the conserved active site residues, Tyr44 and Ser207, respectively. The apoenzyme crystal structure of AlaR consists of three monomers in the asymmetric unit, including a polyethylene glycol molecule in the dimer interface that surrounds one of the His 293 residues and also sits close to one side of the His 293 residue in the opposite monomer. Our results provide structural insights into AlaR that may be used for the development of new antibiotics targeting the alanine racemase in pathogenic bacteria.

    Organizational Affiliation: 

    Biomedical Research Center, Life Science Division, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, South Korea.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alanine racemaseA, B, C371Enterococcus faecalisMutation(s): 1 
Gene Names: alr, EF_0849
EC: 5.1.1.1
UniProt
Find proteins for Q837J0 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q837J0 
Go to UniProtKB:  Q837J0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ837J0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2PE
Query on 2PE
Download Ideal Coordinates CCD File 
I [auth C]NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N		 Ligand Interaction
PLP
Query on PLP
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]		PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N		 Ligand Interaction
EPE
Query on EPE
Download Ideal Coordinates CCD File 
F [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
PPI
Query on PPI
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C]		PROPANOIC ACID
C3 H6 O2
XBDQKXXYIPTUBI-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.232 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.634α = 90
b = 156.516β = 90
c = 147.878γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations